Variant report

Variant	rs17479393
Chromosome Location	chr2:145653287-145653288
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10928232	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs10928235	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11680871	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11682379	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11684042	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1371044	0.89[EUR][1000 genomes]
rs1438896	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[ASN][1000 genomes]
rs1438898	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2077917	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4662402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs55944332	0.84[EUR][1000 genomes]
rs58117425	0.88[EUR][1000 genomes]
rs6738560	0.89[ASN][1000 genomes]
rs72854415	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72854416	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72854462	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9646682	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17479393	KIAA0664L3	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145651800-145653800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr2:145652200-145654200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:145652200-145654200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:145652400-145653600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:145652600-145654000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:145653000-145653400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:145653000-145654400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:145653200-145653400	Flanking Active TSS	NHDF-Ad	bronchial
9	chr2:145653200-145654000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr2:145653200-145654400	Enhancers	Fetal Brain Female	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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